[Chimera-users] questions on find hbond, find clashes/contact

Harinathachari Bahudhanapati hbahudha at fau.edu
Fri Apr 25 15:49:25 PDT 2008

Dear chimera support,
                              I am a huge fan of chimera and I have so 
say I spend a lot of time on chimera these days, as a part of writing 
for my dissertation. I have a few questions and I sincerely you to 
request to help me out.

1. About findHbond: I never seem to get this one right. I model 
Enzyme-inhibitor complexes on patchdock. The inhibitor templates are 
either pdbs from rcsb or modelled on swissmodel. I am not able to 
locate or find any hbonds newly formed in the docked models, when I 
search for intermodel hbonds (I am looking for protein-protein 
interactions). Are there any special criteria or am I missing some 
thing? I want something similar to that of the output of HBPLUS (I 
never seem to get this working either - very frustrating)

2. About find clashes: What are the ideal parameters for clashes and 
contacts. I tried several things, they give me several no of overlaps 
for several different parameters. Are these vanderwaals interactions?  
because some times I see more than 40 interactions between two residues 
-i.e., between the atoms of Enzyme and inhibitor? How reliable are 
these interactions (I need to publish my data) This tool does not seem 
to work unless I add hydrogens to both the chains. 

3. It would be great, if there was a energy minimization tool in 
chimera because I introduce mutations. Please kindly suggest me if 
there are any easy to use tools for this. I tried COOT and 
swisspdbviewer, but not really that user-friendly. 

I read all the newsletter e-mails from CHIMERA users-list everyday. 
Thanks to Elaine, tom, eric and conrad. You guys rock..

hbahudha at fau.edu

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